SMTL ID : 2w27.1

CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN EAL DOMAIN, IN COMPLEX WITH SUBSTRATE C-DI-GMP AND CALCIUM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

4 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 14 residues within 4Å: Chain A: Q.43, E.57, L.59, R.61, N.112, Q.201, D.234, I.235, E.236, G.254, Y.255, P.260 Ligands: 5GP.2, CA.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.43, A:R.61, A:N.112, A:D.234, A:Y.255 Salt bridges: A:D.234, A:E.236 pi-Stacking: A:Y.255, A:Y.255 5GP.2: 11 residues within 4Å: Chain A: V.58, L.59, G.60, R.61, S.70, G.72, F.75, D.89, I.92, N.112 Ligands: 5GP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.60, A:S.70 Salt bridges: A:R.61, A:D.89 pi-Stacking: A:F.75 pi-Cation interactions: A:F.75 5GP.4: 12 residues within 4Å: Chain B: Q.43, E.57, L.59, N.112, D.234, I.235, E.236, G.254, Y.255, P.260 Ligands: 5GP.5, CA.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.43, B:R.61, B:Y.255 Salt bridges: B:D.234, B:E.236 pi-Stacking: B:Y.255, B:Y.255 5GP.5: 10 residues within 4Å: Chain B: L.59, G.60, R.61, S.70, G.72, F.75, D.89, I.92, N.112 Ligands: 5GP.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.60, B:S.70, B:N.112 Salt bridges: B:R.61, B:D.89 pi-Stacking: B:F.75 pi-Cation interactions: B:F.75

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: E.57, N.112, E.146, D.176, K.197 Ligands: 5GP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.57, A:E.146, 5GP.1 CA.6: 5 residues within 4Å: Chain B: E.57, N.112, E.146, D.176 Ligands: 5GP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.57, B:E.146, 5GP.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., Crystal Structures of Ykui and its Complex with Second Messenger C-Di-Gmp Suggests Catalytic Mechanism of Phosphodiester Bond Cleavage by Eal Domains. J.Biol.Chem. (2009)

Release Date

2009-02-24

Peptides

YKUI PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

YKUI PROTEIN

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